RRBSeq: (e)RRBS settings for dmrseq

In trichelab/biscuitEater: Convenience Functions for Biscuit

(e)RRBS settings for dmrseq

Description

(e)RRBS settings for dmrseq

Usage

RRBSeq(bsseq, testCovariate, cutoff = 0.2, bpSpan = 750, ...)

Arguments

bsseq	A bsseq object
testCovariate	The pData column to test on
cutoff	The minimum CpG-wise difference to use (DEFAULT: 0.2)
bpSpan	Span of smoother AND max gap in DMR CpGs (DEFAULT: 750)
...	Other arguments to pass along to dmrseq

Value

          A GRanges object (same as from dmrseq)

Examples

  data(BS.chr21, package="dmrseq")
  dat <- BS.chr21

  rrbs <- RRBSeq(dat[1:500, ], "Rep", cutoff = 0.05, BPPARAM=BiocParallel::SerialParam())

trichelab/biscuitEater documentation built on March 2, 2024, 6:57 p.m.